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dasper

Detecting Aberrant Splicing Events from RNA-sequencing data

https://github.com/dzhang32/dasper

Science Score: 33.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 6 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.8%) to scientific vocabulary

Keywords

diagnostics rare-disease rna-seq-analysis splicing

Keywords from Contributors

bioconductor-package gene bioconductor derfinder rnaseq annotation-agnostic count exon human illumina
Last synced: 6 months ago · JSON representation

Repository

Detecting Aberrant Splicing Events from RNA-sequencing data

Basic Info
Statistics
  • Stars: 16
  • Watchers: 2
  • Forks: 3
  • Open Issues: 5
  • Releases: 2
Topics
diagnostics rare-disease rna-seq-analysis splicing
Created almost 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing Code of conduct Support

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# dasper


[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
[![R build status](https://github.com/dzhang32/dasper/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/dzhang32/dasper/actions/workflows/check-bioc.yml)
[![Codecov test coverage](https://codecov.io/gh/dzhang32/dasper/branch/master/graph/badge.svg)](https://codecov.io/gh/dzhang32/dasper?branch=master)
[![BioC status](http://www.bioconductor.org/shields/build/release/bioc/dasper.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/dasper)
[![DOI](https://zenodo.org/badge/245168125.svg)](https://zenodo.org/badge/latestdoi/245168125)


The aim of `dasper` is to **d**etect **a**berrant **sp**licing **e**vents from **R**NA-seq data. By comparing patient RNA-seq data to a set of controls, `dasper` will score each splicing event in the patient representing the degree to which that splicing event looks abnormal. For a detailed guide on the usage of `dasper`, check out the vignette [here](https://dzhang32.github.io/dasper/articles/dasper.html). 

## Installation instructions

Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `dasper` from [Bioconductor](http://bioconductor.org/) using the following code:

```{r 'install', eval = FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("dasper")
```

And the development version from [GitHub](https://github.com/) with:

```{r 'install_dev', eval = FALSE}
BiocManager::install("dzhang32/dasper")
```

## Citation

Below is the citation output from using `citation('dasper')` in R. Please
run this yourself to check for any updates on how to cite __dasper__.

```{r 'citation', eval = requireNamespace('dasper')}
print(citation("dasper"), bibtex = TRUE)
```

Please note that the `dasper` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

## Code of Conduct

Please note that the `dasper` project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

## Development tools

* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, `r BiocStyle::Githubpkg('r-hub/sysreqs')` and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.
* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.
* The [documentation website](http://dzhang32.github.io/dasper) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.
* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.
* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.

For more details, check the `dev` directory.

In particular, I am very grateful to [Leo](http://lcolladotor.github.io/) for his time and advice throughout the development of `dasper`. The transition of `dasper` Bioconductor-friendly package was made possible thanks to his `r BiocStyle::Biocpkg('biocthis')` package.

Owner

  • Name: David Zhang
  • Login: dzhang32
  • Kind: user
  • Location: London
  • Company: CoSyne Therapeutics

Senior bioinformatics software engineer

GitHub Events

Total
  • Issues event: 1
  • Watch event: 1
  • Push event: 2
Last Year
  • Issues event: 1
  • Watch event: 1
  • Push event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 334
  • Total Committers: 6
  • Avg Commits per committer: 55.667
  • Development Distribution Score (DDS): 0.246
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
David Zhang d****2@u****k 252
David Zhang d****2@g****m 70
Nitesh Turaga n****a@g****m 6
Leonardo Collado Torres l****r@g****m 4
Hervé Pagès h****b@g****m 1
aleighbrown b****h@g****m 1
Committer Domains (Top 20 + Academic)
ucl.ac.uk: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 7
  • Total pull requests: 1
  • Average time to close issues: 12 days
  • Average time to close pull requests: about 19 hours
  • Total issue authors: 7
  • Total pull request authors: 1
  • Average comments per issue: 1.14
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 6 days
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • biga94 (1)
  • pcantalupo (1)
  • lcolladotor (1)
  • AlexBlais74 (1)
  • laurensvdwiel (1)
  • ilakya-selvarajan (1)
  • SMM02 (1)
Pull Request Authors
  • aleighbrown (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 2,761 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
bioconductor.org: dasper

Detecting abberant splicing events from RNA-sequencing data

  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 2,761 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 26.4%
Downloads: 79.2%
Maintainers (1)
david.zhang.12@ucl.ac.uk
Last synced: 11 months ago

Dependencies

.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
DESCRIPTION cran
  • R >= 4.0 depends
  • BiocFileCache * imports
  • BiocParallel * imports
  • GenomeInfoDb * imports
  • GenomicFeatures * imports
  • GenomicRanges * imports
  • IRanges * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • basilisk * imports
  • data.table * imports
  • dplyr * imports
  • ggplot2 * imports
  • ggpubr * imports
  • ggrepel * imports
  • grid * imports
  • magrittr * imports
  • megadepth * imports
  • methods * imports
  • plyranges * imports
  • readr * imports
  • reticulate * imports
  • rtracklayer * imports
  • stringr * imports
  • tidyr * imports
  • AnnotationFilter * suggests
  • BiocStyle * suggests
  • GenomicState * suggests
  • RefManageR * suggests
  • covr * suggests
  • ensembldb * suggests
  • knitr * suggests
  • lifecycle * suggests
  • markdown * suggests
  • recount * suggests
  • rmarkdown * suggests
  • sessioninfo * suggests
  • testthat * suggests
  • tibble * suggests
Dockerfile docker
  • bioconductor/bioconductor_docker RELEASE_3_13 build